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Table S1. List of differentially expressed genes between biofilm and planktonic populations with a false discovery rate of 0.05. A positive gene effect indicated higher expression in biofilm versus planktonic. Genes were annotated using a variety of databases as described in the main text.

Table S2. Analysis of the percentage of each functional category within the B. thetaiotaomicron genome and within the group of differentially genes (dexpr) between planktonic and biofilm-associated cells. Groups marked with an * were significantly enriched in the differentially expressed genes as determined using a hypergeometric distribution.

Table S3. Annotated list of genes within polysaccharide utilization loci (PULs) including ranking based on average change in expression, gene effect of differentially expressed genes, and gene descriptions.

Table S4. List of differentially expressed genes within capsular polysaccharide synthesis (CPS) loci, annotated with gene effect and P-value.

Table S5. Annotated list of datasets used in clustering analysis, including relevant experimental information and GEO accession numbers. Dataset 1: comparison of cells grown with glucose or PMG glycans in different culture volumes (Martens et al., 2008). Dataset 2: comparison of strains with various sigma factors knocked out, grown on glucose or glycans (Martens et al., 2009). Dataset 3: comparison of wild type and a chuR knockout strain, grown in gnotobiotic mouse ceca. Dataset 4: comparison of cells harvested before and after lactose addition to the growth medium. Dataset 5: comparison of cells grown in different medium types or in mouse ceca.

Table S6. Full list of key clustering genes with annotations.

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